Nadeem Faruque

11 papers Journal 11
YearRankTypeTitle / Venue / Authors
2012 J jnl
J. Bioinform. Comput. Biol.
Irina I. Abnizova, Steven Leonard, Tom Skelly, Andy Brown, David K. Jackson, Marina Gourtovaia, Guoying Qi, Rene te Boekhorst, Nadeem Faruque, Kevin Lewis, Tony Cox
2012 J jnl
Nucleic Acids Res.
Clara Amid, Ewan Birney, Lawrence Bower, Ana Cerdeño-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Richard Gibson, Neil Goodgame, Christopher I. Hunter, Mikyung Jang, Rasko Leinonen, Xin Liu, Arnaud Oisel, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Stéphane Rivière, Marc Rossello, Alexander Senf, Dimitriy Smirnov, Petra ten Hoopen, Daniel Vaughan, Robert Vaughan, Vadim Zalunin, Guy Cochrane
2011 J jnl
Nucleic Acids Res.
Rasko Leinonen, Ruth Akhtar, Ewan Birney, Lawrence Bower, Ana Cerdeño-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Mikyung Jang, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Siamak Sobhany, Petra ten Hoopen, Robert Vaughan, Vadim Zalunin, Guy Cochrane
2010 J jnl
Nucleic Acids Res.
Rasko Leinonen, Ruth Akhtar, Ewan Birney, James K. Bonfield, Lawrence Bower, Matthew Corbett, Ying Cheng, Fehmi Demiralp, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Christopher I. Hunter, Mikyung Jang, Steven Leonard, Quan Lin, Rodrigo Lopez, Michael Maguire, Hamish McWilliam, Sheila Plaister, Rajesh Radhakrishnan, Siamak Sobhany, Guy Slater, Petra ten Hoopen, Franck Valentin, Robert Vaughan, Vadim Zalunin, Daniel R. Zerbino, Guy Cochrane
2009 J jnl
Nucleic Acids Res.
Guy Cochrane, Ruth Akhtar, James K. Bonfield, Lawrence Bower, Fehmi Demiralp, Nadeem Faruque, Richard Gibson, Gemma Hoad, Tim J. P. Hubbard, Christopher I. Hunter, Mikyung Jang, Szilveszter Juhos, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Sheila Plaister, Rajesh Radhakrishnan, Stephen Robinson, Siamak Sobhany, Petra ten Hoopen, Robert Vaughan, Vadim Zalunin, Ewan Birney
2008 J jnl
Nucleic Acids Res.
Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, James K. Bonfield, Lawrence Bower, Paul Browne, Matias Castro, Tony Cox, Fehmi Demiralp, Ruth Y. Eberhardt, Nadeem Faruque, Gemma Hoad, Mikyung Jang, Tamara Kulikova, Alberto Labarga, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Sheila Plaister, Stephen Robinson, Siamak Sobhany, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler, Tim J. P. Hubbard, Ewan Birney
2007 J jnl
Nucleic Acids Res.
Tamara Kulikova, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Lawrence Bower, Paul Browne, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Y. Eberhardt, Nadeem Faruque, Gemma Hoad, Carola Kanz, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Sheila Plaister, Siamak Sobhany, Peter Stoehr, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler
2006 J jnl
Nucleic Acids Res.
Guy Cochrane, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Wendy Baker, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Paul Browne, Alexandra van den Broek, Matias Castro, Karyn Duggan, Ruth Y. Eberhardt, Nadeem Faruque, John Gamble, Carola Kanz, Tamara Kulikova, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Michelle McHale, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Siamak Sobhany, Peter Stoehr, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler
2005 J jnl
Nucleic Acids Res.
Paul J. Kersey, Lawrence Bower, Lorna Morris, Alan Horne, Robert Petryszak, Carola Kanz, Alexander Kanapin, Ujjwal Das, Karine Michoud, Isabelle Phan, Alexandre Gattiker, Tamara Kulikova, Nadeem Faruque, Karyn Duggan, Peter McLaren, Britt Reimholz, Laurent Duret, Simon Penel, Ingmar Reuter, Rolf Apweiler
2005 J jnl
Nucleic Acids Res.
Carola Kanz, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Alastair Baldwin, Kirsty Bates, Paul Browne, Alexandra van den Broek, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Y. Eberhardt, Nadeem Faruque, John Gamble, Federico Garcia Diez, Nicola Harte, Tamara Kulikova, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Siamak Sobhany, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler
2004 J jnl
Nucleic Acids Res.
Tamara Kulikova, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Kirsty Bates, Paul Browne, Alexandra van den Broek, Guy Cochrane, Karyn Duggan, Ruth Y. Eberhardt, Nadeem Faruque, Maria Garcia-Pastor, Nicola Harte, Carola Kanz, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Peter Stoehr, Guenter Stoesser, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler
tests/integration/test_elf_extractor.py
← Index tests/integration/test_elf_extractor.py python
"""
Integration tests for the ELFExtractor base class.
"""
import pytest
from unittest.mock import Mock, patch, MagicMock

pytestmark = [pytest.mark.integration, pytest.mark.elf]


class TestELFExtractorInitialization:
    """Tests for ELFExtractor initialization."""

    def test_elf_extractor_with_valid_elf(self, elf_binary_path, mock_logger):
        """Test ELFExtractor initialization with valid ELF file."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            assert extractor.filepath == elf_binary_path
            assert extractor._is_elf_file() is True

    def test_elf_extractor_with_invalid_file(self, pe_binary_path, mock_logger):
        """Test ELFExtractor initialization with non-ELF file."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(pe_binary_path, mock_logger)

            # Should not be a valid ELF
            assert extractor._is_elf_file() is False

    def test_elf_extractor_with_text_file(self, temp_text_file, mock_logger):
        """Test ELFExtractor initialization with text file."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(temp_text_file, mock_logger)

            # Should not be a valid ELF
            assert extractor._is_elf_file() is False


class TestELFExtractorMethods:
    """Tests for ELFExtractor helper methods."""

    def test_is_elf_file_true(self, elf_binary_path, mock_logger):
        """Test _is_elf_file returns True for valid ELF."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            assert extractor._is_elf_file() is True

    def test_is_elf_file_cached(self, elf_binary_path, mock_logger):
        """Test _is_elf_file result is cached."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            # First call
            result1 = extractor._is_elf_file()
            # Second call should use cached value
            result2 = extractor._is_elf_file()

            assert result1 == result2
            # Cache should be set
            assert extractor._elf_file_valid is not None

    def test_is_64bit(self, elf_binary_path, mock_logger):
        """Test _is_64bit method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._is_64bit()
            # Result depends on the test binary
            assert isinstance(result, bool)

    def test_is_stripped(self, elf_binary_path, mock_logger):
        """Test _is_stripped method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._is_stripped()
            assert isinstance(result, bool)

    def test_has_debug_info(self, elf_binary_path, mock_logger):
        """Test _has_debug_info method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._has_debug_info()
            assert isinstance(result, bool)

    def test_get_architecture(self, elf_binary_path, mock_logger):
        """Test _get_architecture method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._get_architecture()
            # Should return a string (architecture name)
            assert isinstance(result, str)
            assert result != ""

    def test_get_endianness(self, elf_binary_path, mock_logger):
        """Test _get_endianness method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._get_endianness()
            # Should be one of: "little", "big", or "unknown"
            assert result in ["little", "big", "unknown"]

    def test_get_file_type(self, elf_binary_path, mock_logger):
        """Test _get_file_type method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._get_file_type()
            # Should return a file type string
            assert isinstance(result, str)
            # Common values: "executable", "shared_object", "relocatable", etc.
            expected_types = ["none", "relocatable", "executable", "shared_object", "core_dump", "unknown"]
            assert result in expected_types or result.startswith("ET_")

    def test_is_pie(self, elf_binary_path, mock_logger):
        """Test _is_pie method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._is_pie()
            assert isinstance(result, bool)

    def test_has_stack_protection(self, elf_binary_path, mock_logger):
        """Test _has_stack_protection method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._has_stack_protection()
            assert isinstance(result, bool)

    def test_has_nx_bit(self, elf_binary_path, mock_logger):
        """Test _has_nx_bit method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._has_nx_bit()
            assert isinstance(result, bool)

    def test_has_relro(self, elf_binary_path, mock_logger):
        """Test _has_relro method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._has_relro()
            assert isinstance(result, bool)

    def test_get_build_id(self, elf_binary_path, mock_logger):
        """Test _get_build_id method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._get_build_id()
            # Could be None if no build ID, or a hex string
            assert result is None or isinstance(result, str)

    def test_count_sections(self, elf_binary_path, mock_logger):
        """Test _count_sections method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._count_sections()
            assert isinstance(result, int)
            assert result >= 0

    def test_count_segments(self, elf_binary_path, mock_logger):
        """Test _count_segments method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._count_segments()
            assert isinstance(result, int)
            assert result >= 0

    def test_count_symbols(self, elf_binary_path, mock_logger):
        """Test _count_symbols method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._count_symbols()
            assert isinstance(result, int)
            assert result >= 0

    def test_get_dependencies(self, elf_binary_path, mock_logger):
        """Test _get_dependencies method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor._get_dependencies()
            assert isinstance(result, list)


class TestWithELFFile:
    """Tests for the _with_elf_file context manager method."""

    def test_with_elf_file_success(self, elf_binary_path, mock_logger):
        """Test _with_elf_file executes operation successfully."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            # Define a simple operation
            def get_header(elf):
                return elf.header is not None

            result = extractor._with_elf_file(get_header)
            assert result is True

    def test_with_elf_file_error_handling(self, temp_text_file, mock_logger):
        """Test _with_elf_file handles errors gracefully."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(temp_text_file, mock_logger)

            # Define an operation that would fail
            def get_header(elf):
                return elf.header

            result = extractor._with_elf_file(get_header)
            # Should return None on error
            assert result is None


class TestELFExtractorTag:
    """Tests for tag method in ELF extractors."""

    def test_elf_features_tag(self, elf_binary_path, mock_logger):
        """Test that ELFFeaturesExtractor returns correct tag."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)
            tag = extractor.tag()
            # Should return the tag string
            assert isinstance(tag, str)
            assert "elf" in tag.lower() or "features" in tag.lower()


class TestELFExtractorClickHouseTable:
    """Tests for get_clickhouse_table method in ELF extractors."""

    def test_elf_features_clickhouse_table(self, elf_binary_path, mock_logger):
        """Test that ELFFeaturesExtractor returns correct ClickHouse table name."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)
            assert extractor.get_clickhouse_table() == "redb_elf_features"


class TestELFExtractorExtract:
    """Tests for extract method in ELF extractors."""

    def test_elf_features_extract(self, elf_binary_path, mock_logger):
        """Test ELFFeaturesExtractor.extract() returns valid data."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor
        from redb.models.dataclasses import ELFFeatures

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            result = extractor.extract()
            assert result is not None
            assert isinstance(result, ELFFeatures)

            # Check some expected fields
            assert isinstance(result.ei_class, int)
            assert isinstance(result.ei_data, int)
            assert isinstance(result.e_entry, int)
            assert isinstance(result.number_of_sections, int)
            assert isinstance(result.number_of_segments, int)

    def test_elf_features_extract_invalid_file(self, pe_binary_path, mock_logger):
        """Test ELFFeaturesExtractor.extract() handles invalid ELF."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(pe_binary_path, mock_logger)

            result = extractor.extract()
            # Should return None for invalid ELF
            assert result is None


class TestELFExtractorPrepareExportData:
    """Tests for prepare_export_data method in ELF extractors."""

    def test_elf_features_prepare_export_elasticsearch(self, elf_binary_path, mock_logger):
        """Test prepare_export_data for Elasticsearch."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            # First extract
            extractor.extract()
            result = extractor.prepare_export_data("ElasticsearchExporter")
            # Should return the elf_features dataclass
            assert result is extractor.elf_features

    def test_elf_features_prepare_export_clickhouse(self, elf_binary_path, mock_logger):
        """Test prepare_export_data for ClickHouse."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)

            # First extract
            extractor.extract()
            result = extractor.prepare_export_data("ClickHouseExporter")

            # Should return tuple of (data, column_names, column_type_names)
            assert isinstance(result, tuple)
            assert len(result) == 3
            data, column_names, column_type_names = result
            assert isinstance(data, list)
            assert isinstance(column_names, list)
            assert isinstance(column_type_names, list)
            # Column names and types should match in length
            assert len(column_names) == len(column_type_names)


class TestELFExtractorAdvanced:
    """Advanced tests for ELF extraction using hello_advanced binary."""

    def test_elf_advanced_features(self, elf_advanced_binary_path, mock_logger):
        """Test ELFFeaturesExtractor with more complex ELF binary."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_advanced_binary_path, mock_logger)

            result = extractor.extract()
            assert result is not None

            # Check that we can extract meaningful data
            assert result.number_of_sections > 0
            assert result.number_of_segments > 0

    def test_elf_advanced_architecture(self, elf_advanced_binary_path, mock_logger):
        """Test architecture detection for advanced ELF binary."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_advanced_binary_path, mock_logger)

            arch = extractor._get_architecture()
            # Should detect a valid architecture
            assert arch != "unknown"
            assert arch != ""